Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes

Susan E. Tsutakawa, David S. Shin, Clifford D. Mol, Tadahide Izumi, Andrew S. Arvai, Anil K. Mantha, Bartosz Szczesny, Ivaylo N. Ivanov, David J. Hosfield, Buddhadev Maiti, Mike E. Pique, Kenneth A. Frankel, Kenichi Hitomi, Richard P. Cunningham, Sankar Mitra, John A. Tainer

Research output: Contribution to journalArticle

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Abstract

Non-coding apurinic/apyrimidinic (AP) sites in DNA form spontaneously and as DNA base excision repair intermediates are the most common toxic and mutagenic in vivo DNA lesion. For repair,APsites must be processed by 5' AP endonucleases in initial stages of base repair. Human APE1 and bacterial Nfo represent the two conserved 5' AP endonuclease families in the biosphere; they both recognize AP sites and incise the phosphodiester backbone 5' to the lesion, yet they lack similar structures and metal ion requirements. Here, we determined and analyzed crystal structures of a 2.4 Å resolution APE1-DNA product complex with Mg2+ and a 0.92 Å Nfo with three metal ions. Structural and biochemical comparisons of these two evolutionarily distinct enzymes characterize keyAPE1catalytic residues that are potentially functionally similar to Nfo active site components, as further tested and supported by computational analyses. We observe a magnesium-water cluster in the APE1 active site, with only Glu-96 forming the direct protein coordination to the Mg2+. Despite differences in structure and metal requirements of APE1 and Nfo, comparison of their active site structures surprisingly reveals strong geometric conservation of the catalytic reaction, with APE1 catalytic side chains positioned analogously to Nfo metal positions, suggesting surprising functional equivalence between Nfo metal ions and APE1 residues. The finding that APE1 residues are positioned to substitute for Nfo metal ions is supported by the impact of mutations on activity. Collectively, the results illuminate the activities of residues, metal ions, and active site features for abasic site endonucleases.

Original languageEnglish
Pages (from-to)8445-8455
Number of pages11
JournalJournal of Biological Chemistry
Volume288
Issue number12
DOIs
StatePublished - Mar 22 2013

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Deoxyribonuclease IV (Phage T4-Induced)
DNA-(Apurinic or Apyrimidinic Site) Lyase
DNA Repair Enzymes
Endonucleases
Metal ions
Metals
Ions
Repair
Catalytic Domain
DNA
Poisons
Magnesium
Conservation
Crystal structure
DNA Repair
Water
Enzymes
Mutation

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. / Tsutakawa, Susan E.; Shin, David S.; Mol, Clifford D.; Izumi, Tadahide; Arvai, Andrew S.; Mantha, Anil K.; Szczesny, Bartosz; Ivanov, Ivaylo N.; Hosfield, David J.; Maiti, Buddhadev; Pique, Mike E.; Frankel, Kenneth A.; Hitomi, Kenichi; Cunningham, Richard P.; Mitra, Sankar; Tainer, John A.

In: Journal of Biological Chemistry, Vol. 288, No. 12, 22.03.2013, p. 8445-8455.

Research output: Contribution to journalArticle

Tsutakawa, SE, Shin, DS, Mol, CD, Izumi, T, Arvai, AS, Mantha, AK, Szczesny, B, Ivanov, IN, Hosfield, DJ, Maiti, B, Pique, ME, Frankel, KA, Hitomi, K, Cunningham, RP, Mitra, S & Tainer, JA 2013, 'Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes', Journal of Biological Chemistry, vol. 288, no. 12, pp. 8445-8455. https://doi.org/10.1074/jbc.M112.422774
Tsutakawa, Susan E. ; Shin, David S. ; Mol, Clifford D. ; Izumi, Tadahide ; Arvai, Andrew S. ; Mantha, Anil K. ; Szczesny, Bartosz ; Ivanov, Ivaylo N. ; Hosfield, David J. ; Maiti, Buddhadev ; Pique, Mike E. ; Frankel, Kenneth A. ; Hitomi, Kenichi ; Cunningham, Richard P. ; Mitra, Sankar ; Tainer, John A. / Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. In: Journal of Biological Chemistry. 2013 ; Vol. 288, No. 12. pp. 8445-8455.
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abstract = "Non-coding apurinic/apyrimidinic (AP) sites in DNA form spontaneously and as DNA base excision repair intermediates are the most common toxic and mutagenic in vivo DNA lesion. For repair,APsites must be processed by 5' AP endonucleases in initial stages of base repair. Human APE1 and bacterial Nfo represent the two conserved 5' AP endonuclease families in the biosphere; they both recognize AP sites and incise the phosphodiester backbone 5' to the lesion, yet they lack similar structures and metal ion requirements. Here, we determined and analyzed crystal structures of a 2.4 {\AA} resolution APE1-DNA product complex with Mg2+ and a 0.92 {\AA} Nfo with three metal ions. Structural and biochemical comparisons of these two evolutionarily distinct enzymes characterize keyAPE1catalytic residues that are potentially functionally similar to Nfo active site components, as further tested and supported by computational analyses. We observe a magnesium-water cluster in the APE1 active site, with only Glu-96 forming the direct protein coordination to the Mg2+. Despite differences in structure and metal requirements of APE1 and Nfo, comparison of their active site structures surprisingly reveals strong geometric conservation of the catalytic reaction, with APE1 catalytic side chains positioned analogously to Nfo metal positions, suggesting surprising functional equivalence between Nfo metal ions and APE1 residues. The finding that APE1 residues are positioned to substitute for Nfo metal ions is supported by the impact of mutations on activity. Collectively, the results illuminate the activities of residues, metal ions, and active site features for abasic site endonucleases.",
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AU - Mol, Clifford D.

AU - Izumi, Tadahide

AU - Arvai, Andrew S.

AU - Mantha, Anil K.

AU - Szczesny, Bartosz

AU - Ivanov, Ivaylo N.

AU - Hosfield, David J.

AU - Maiti, Buddhadev

AU - Pique, Mike E.

AU - Frankel, Kenneth A.

AU - Hitomi, Kenichi

AU - Cunningham, Richard P.

AU - Mitra, Sankar

AU - Tainer, John A.

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N2 - Non-coding apurinic/apyrimidinic (AP) sites in DNA form spontaneously and as DNA base excision repair intermediates are the most common toxic and mutagenic in vivo DNA lesion. For repair,APsites must be processed by 5' AP endonucleases in initial stages of base repair. Human APE1 and bacterial Nfo represent the two conserved 5' AP endonuclease families in the biosphere; they both recognize AP sites and incise the phosphodiester backbone 5' to the lesion, yet they lack similar structures and metal ion requirements. Here, we determined and analyzed crystal structures of a 2.4 Å resolution APE1-DNA product complex with Mg2+ and a 0.92 Å Nfo with three metal ions. Structural and biochemical comparisons of these two evolutionarily distinct enzymes characterize keyAPE1catalytic residues that are potentially functionally similar to Nfo active site components, as further tested and supported by computational analyses. We observe a magnesium-water cluster in the APE1 active site, with only Glu-96 forming the direct protein coordination to the Mg2+. Despite differences in structure and metal requirements of APE1 and Nfo, comparison of their active site structures surprisingly reveals strong geometric conservation of the catalytic reaction, with APE1 catalytic side chains positioned analogously to Nfo metal positions, suggesting surprising functional equivalence between Nfo metal ions and APE1 residues. The finding that APE1 residues are positioned to substitute for Nfo metal ions is supported by the impact of mutations on activity. Collectively, the results illuminate the activities of residues, metal ions, and active site features for abasic site endonucleases.

AB - Non-coding apurinic/apyrimidinic (AP) sites in DNA form spontaneously and as DNA base excision repair intermediates are the most common toxic and mutagenic in vivo DNA lesion. For repair,APsites must be processed by 5' AP endonucleases in initial stages of base repair. Human APE1 and bacterial Nfo represent the two conserved 5' AP endonuclease families in the biosphere; they both recognize AP sites and incise the phosphodiester backbone 5' to the lesion, yet they lack similar structures and metal ion requirements. Here, we determined and analyzed crystal structures of a 2.4 Å resolution APE1-DNA product complex with Mg2+ and a 0.92 Å Nfo with three metal ions. Structural and biochemical comparisons of these two evolutionarily distinct enzymes characterize keyAPE1catalytic residues that are potentially functionally similar to Nfo active site components, as further tested and supported by computational analyses. We observe a magnesium-water cluster in the APE1 active site, with only Glu-96 forming the direct protein coordination to the Mg2+. Despite differences in structure and metal requirements of APE1 and Nfo, comparison of their active site structures surprisingly reveals strong geometric conservation of the catalytic reaction, with APE1 catalytic side chains positioned analogously to Nfo metal positions, suggesting surprising functional equivalence between Nfo metal ions and APE1 residues. The finding that APE1 residues are positioned to substitute for Nfo metal ions is supported by the impact of mutations on activity. Collectively, the results illuminate the activities of residues, metal ions, and active site features for abasic site endonucleases.

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